library(knn.covertree)
library(pbapply)
library(ggplot2)
dropout_percent <- c(0,5,10,20,30,40,50,75,80,85,90,95)
counts_path <- sapply(dropout_percent, function(y) paste0("/Users/elise/Desktop/GitHub/Hubness_sc/bulkRNAseq/simul",y,".csv"))
pca_path <- sapply(dropout_percent, function(y) paste0("/Users/elise/Desktop/GitHub/Hubness_sc/bulkRNAseq/simul_pca_readyforhubness",y,".csv"))
sdev_path <- sapply(dropout_percent, function(y) paste0("/Users/elise/Desktop/GitHub/Hubness_sc/bulkRNAseq/simul_pca_sdev",y,".csv"))
simul <- pblapply(counts_path, function(x) read.table(x))
simul_pca <- pblapply(pca_path, function(x) read.table(x))
sdev<-pblapply(sdev_path, function(x) read.table(file=x))
sdev <- pblapply(sdev, function(x) return(x/x[1,1]))
source(file="/Users/elise/Desktop/GitHub/Hubness_sc/R_scripts/load_data/hubness_load_write_data_simul.R")
hubness <- lapply(hubness, function(x) {x$cellID <- names(hubness_scores_data[[1]][[1]][[1]]); return(x)})
get_hub_scores <- function(data,k) {
knn_graph <- knn.covertree::find_knn(t(data),k)
knn_list <- knn_graph$index
occurence <- pbsapply(1:nrow(knn_list), function(x) {sum(knn_list==x)})
return(occurence)
}
asymmetry_evaluation <- function(data) {
knn_graph <- knn.covertree::find_knn(t(data),k)
knn_list <- knn_graph$index
increment = 0
for (i in 1:nrow(knn_list)) {
for (j in 1:ncol(knn_list)) {
if (i %in% knn_list[knn_list[i,j],]) {
increment <- increment + 1
}
}
}
return(1-increment/(nrow(knn_list)*ncol(knn_list)))
}
skewness <- function(distrib) {
return(mean((distrib-mean(distrib))^3)/(sd(distrib)^3))
}
antihub <- function(distrib) {
return(sum(distrib==0))
}
k_thd <- function(distrib,k) {
return(sum(distrib>=2*k))
}
meansd_thd <- function(distrib) {
thd <- mean(distrib) + 3*sd(distrib)
return(sum(distrib>=thd))
}
generate_gaussian <- function(n,dim) {
return(t(sapply(1:dim, function(x) rnorm(n))))
}
generate_uniform <- function(n,dim) {
return(t(sapply(1:dim, function(x) runif(n,min=(-1)))))
}
relative_contrast <- function(data) {
tmp <- as.matrix(dist(t(data)))
diag(tmp) <- NA
rc <- apply(tmp, 1, function(x) abs(max(x, na.rm = T)-min(x, na.rm = T))/min(x, na.rm = T))
return(mean(rc))
}
k=50
dim_val=unique(hubness[[1]]$Dimension)
scores <- pblapply(hubness, function(x) {tmp <- x[x$p==2 & x$k==k,]; score<-pblapply(dim_val, function(y) return(tmp$score[tmp$Dimension==y])); return(score)})
lapply(scores, function(x) lapply(x, hist))
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## $mids
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## $xname
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## $equidist
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## $density
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## $mids
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## $xname
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## $equidist
## [1] TRUE
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## $mids
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## $xname
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## $equidist
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## $density
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## $mids
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## $xname
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## $equidist
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## $mids
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## $xname
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## $equidist
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## $mids
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## $xname
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## $equidist
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## $mids
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## $xname
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## $equidist
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
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##
## [[4]]
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## $breaks
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## $counts
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## $density
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## $xname
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[4]][[2]]
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## $density
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[4]][[3]]
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## $counts
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## $density
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[4]][[4]]
## $breaks
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[4]][[5]]
## $breaks
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## $counts
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## $density
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[4]][[6]]
## $breaks
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## $counts
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## $density
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## $mids
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## $xname
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## $equidist
## [1] TRUE
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## attr(,"class")
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## $breaks
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## $counts
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## $density
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## [6] 1.154163e-04 1.154163e-04 3.297609e-05 0.000000e+00 1.648805e-05
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
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## [[4]][[8]]
## $breaks
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## $breaks
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## $counts
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## $density
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## [6] 1.648805e-05 5.770816e-05 4.946414e-05 8.244023e-06 1.648805e-05
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## $breaks
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## $counts
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## $density
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## $breaks
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## $counts
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## $density
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## [6] 2.308326e-04 2.143446e-04 1.566364e-04 4.122012e-05 8.244023e-06
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## $mids
## [1] 50 150 250 350 450 550 650 750 850 950
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
##
## [[5]]
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## $breaks
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## $counts
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## $density
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## $mids
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## [16] 77.5 82.5
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## $breaks
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## $counts
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## $density
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[5]][[3]]
## $breaks
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## $counts
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## [6] 2.349547e-03 9.068425e-04 3.297609e-04 4.122012e-05 4.122012e-05
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
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## [[5]][[4]]
## $breaks
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## $counts
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[5]][[5]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450
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## $counts
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## $density
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## [6] 1.978566e-04 1.648805e-05 1.648805e-05 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[5]][[6]]
## $breaks
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## $counts
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## $density
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[5]][[7]]
## $breaks
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## $counts
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## $density
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## [6] 8.244023e-05 6.595218e-05 0.000000e+00 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## $breaks
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## $counts
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## [11] 0.000000e+00 0.000000e+00 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525 575 625
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[5]][[9]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750
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## $counts
## [1] 888 158 56 35 36 12 12 2 5 2 3 1 1 0 2
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## $density
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525 575 625 675 725
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[5]][[10]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800
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## $counts
## [1] 885 147 74 38 19 17 10 9 3 2 3 1 1 2 1 1
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## $density
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## [16] 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525 575 625 675 725 775
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[5]][[11]]
## $breaks
## [1] 0 100 200 300 400 500 600 700 800 900 1000
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## $counts
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## $density
## [1] 9.175598e-03 0.000000e+00 8.244023e-06 4.122012e-05 1.401484e-04
## [6] 2.143446e-04 2.061006e-04 1.566364e-04 4.946414e-05 8.244023e-06
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## $mids
## [1] 50 150 250 350 450 550 650 750 850 950
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
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##
## [[6]]
## [[6]][[1]]
## $breaks
## [1] 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85
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## $counts
## [1] 5 21 32 40 61 90 86 107 110 143 145 171 122 64 13 3
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## $density
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## [6] 0.0148392415 0.0141797197 0.0176422094 0.0181368508 0.0235779060
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## [16] 0.0004946414
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## $mids
## [1] 7.5 12.5 17.5 22.5 27.5 32.5 37.5 42.5 47.5 52.5 57.5 62.5 67.5 72.5 77.5
## [16] 82.5
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
##
## [[6]][[2]]
## $breaks
## [1] 0 10 20 30 40 50 60 70 80 90 100
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## $counts
## [1] 23 76 140 167 203 207 172 150 68 7
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## $density
## [1] 0.0018961253 0.0062654575 0.0115416323 0.0137675185 0.0167353669
## [6] 0.0170651278 0.0141797197 0.0123660346 0.0056059357 0.0005770816
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## $mids
## [1] 5 15 25 35 45 55 65 75 85 95
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## $density
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## $mids
## [1] 10 30 50 70 90 110 130 150 170
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## [1] "histogram"
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## [[6]][[4]]
## $breaks
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## $counts
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## $density
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## [6] 6.595218e-05 3.297609e-05 0.000000e+00 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[6]][[5]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500
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## $counts
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## $density
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## [6] 8.244023e-05 0.000000e+00 4.946414e-05 0.000000e+00 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[6]][[6]]
## $breaks
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## $density
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## [6] 1.483924e-04 3.297609e-05 3.297609e-05 3.297609e-05 0.000000e+00
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## [1] "histogram"
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## [[6]][[7]]
## $breaks
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## $density
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## [6] 1.154163e-04 9.892828e-05 1.648805e-05 4.946414e-05
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[6]][[8]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[6]][[9]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550
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## $counts
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## $density
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## [6] 1.319044e-04 1.483924e-04 4.946414e-05 3.297609e-05 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
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## [[6]][[10]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550
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## $counts
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## $density
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[6]][[11]]
## $breaks
## [1] 0 100 200 300 400 500 600 700 800 900
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## $counts
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## $density
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## [6] 2.143446e-04 2.390767e-04 1.401484e-04 5.770816e-05
##
## $mids
## [1] 50 150 250 350 450 550 650 750 850
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
##
## [[7]]
## [[7]][[1]]
## $breaks
## [1] 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80
##
## $counts
## [1] 1 10 19 26 51 62 65 89 103 120 128 177 179 107 65 11
##
## $density
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[7]][[2]]
## $breaks
## [1] 0 10 20 30 40 50 60 70 80 90 100
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## $counts
## [1] 28 63 146 185 169 210 197 152 56 7
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## $density
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## $mids
## [1] 5 15 25 35 45 55 65 75 85 95
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[7]][[3]]
## $breaks
## [1] 0 20 40 60 80 100 120 140 160 180 200
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## $counts
## [1] 236 351 269 145 98 53 32 19 9 1
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## $density
## [1] 9.727947e-03 1.446826e-02 1.108821e-02 5.976917e-03 4.039571e-03
## [6] 2.184666e-03 1.319044e-03 7.831822e-04 3.709810e-04 4.122012e-05
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## $mids
## [1] 10 30 50 70 90 110 130 150 170 190
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[7]][[4]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400
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## $counts
## [1] 788 279 96 20 19 6 4 1
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## $density
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## [6] 9.892828e-05 6.595218e-05 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[7]][[5]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550 600
##
## $counts
## [1] 824 233 94 26 16 10 6 1 1 0 1 1
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## $density
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## [6] 1.648805e-04 9.892828e-05 1.648805e-05 1.648805e-05 0.000000e+00
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525 575
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[7]][[6]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550 600 650
##
## $counts
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## $density
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## [11] 0.000000e+00 0.000000e+00 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525 575 625
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[7]][[7]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550
##
## $counts
## [1] 820 233 86 43 12 9 4 3 0 2 1
##
## $density
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## [6] 1.483924e-04 6.595218e-05 4.946414e-05 0.000000e+00 3.297609e-05
## [11] 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[7]][[8]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550 600 650
##
## $counts
## [1] 837 208 88 39 20 8 7 3 1 1 0 0 1
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## $density
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## [11] 0.000000e+00 0.000000e+00 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525 575 625
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[7]][[9]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500
##
## $counts
## [1] 799 271 80 37 16 5 2 2 0 1
##
## $density
## [1] 1.317395e-02 4.468261e-03 1.319044e-03 6.100577e-04 2.638087e-04
## [6] 8.244023e-05 3.297609e-05 3.297609e-05 0.000000e+00 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375 425 475
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[7]][[10]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700
##
## $counts
## [1] 872 164 71 44 29 9 4 10 3 2 3 1 0 1
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## $density
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## [6] 1.483924e-04 6.595218e-05 1.648805e-04 4.946414e-05 3.297609e-05
## [11] 4.946414e-05 1.648805e-05 0.000000e+00 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525 575 625 675
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[7]][[11]]
## $breaks
## [1] 0 100 200 300 400 500 600 700 800 900
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## $counts
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## $density
## [1] 9.175598e-03 0.000000e+00 0.000000e+00 8.244023e-05 1.648805e-04
## [6] 1.483924e-04 1.731245e-04 1.648805e-04 9.068425e-05
##
## $mids
## [1] 50 150 250 350 450 550 650 750 850
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
##
## [[8]]
## [[8]][[1]]
## $breaks
## [1] 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85
##
## $counts
## [1] 3 8 18 28 52 50 70 81 81 127 136 249 170 84 45 9 2
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## $density
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## $mids
## [1] 2.5 7.5 12.5 17.5 22.5 27.5 32.5 37.5 42.5 47.5 52.5 57.5 62.5 67.5 72.5
## [16] 77.5 82.5
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[8]][[2]]
## $breaks
## [1] 0 10 20 30 40 50 60 70 80 90
##
## $counts
## [1] 28 96 131 155 149 181 259 199 15
##
## $density
## [1] 0.002308326 0.007914262 0.010799670 0.012778236 0.012283594 0.014921682
## [7] 0.021352020 0.016405606 0.001236603
##
## $mids
## [1] 5 15 25 35 45 55 65 75 85
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[8]][[3]]
## $breaks
## [1] 0 20 40 60 80 100 120 140 160 180 200 220 240
##
## $counts
## [1] 270 321 245 158 93 61 37 20 3 1 3 1
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## $density
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## [11] 1.236603e-04 4.122012e-05
##
## $mids
## [1] 10 30 50 70 90 110 130 150 170 190 210 230
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[8]][[4]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450
##
## $counts
## [1] 792 275 95 26 13 5 1 5 1
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## $density
## [1] 1.305853e-02 4.534213e-03 1.566364e-03 4.286892e-04 2.143446e-04
## [6] 8.244023e-05 1.648805e-05 8.244023e-05 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375 425
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[8]][[5]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450
##
## $counts
## [1] 793 259 92 41 13 10 4 0 1
##
## $density
## [1] 1.307502e-02 4.270404e-03 1.516900e-03 6.760099e-04 2.143446e-04
## [6] 1.648805e-04 6.595218e-05 0.000000e+00 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375 425
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[8]][[6]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400
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## $counts
## [1] 789 262 104 32 11 7 5 3
##
## $density
## [1] 1.300907e-02 4.319868e-03 1.714757e-03 5.276175e-04 1.813685e-04
## [6] 1.154163e-04 8.244023e-05 4.946414e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[8]][[7]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450
##
## $counts
## [1] 806 242 93 42 14 7 5 3 1
##
## $density
## [1] 1.328937e-02 3.990107e-03 1.533388e-03 6.924979e-04 2.308326e-04
## [6] 1.154163e-04 8.244023e-05 4.946414e-05 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375 425
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[8]][[8]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550 600
##
## $counts
## [1] 813 237 99 32 15 7 7 1 0 0 1 1
##
## $density
## [1] 1.340478e-02 3.907667e-03 1.632317e-03 5.276175e-04 2.473207e-04
## [6] 1.154163e-04 1.154163e-04 1.648805e-05 0.000000e+00 0.000000e+00
## [11] 1.648805e-05 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525 575
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[8]][[9]]
## $breaks
## [1] 0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300
##
## $counts
## [1] 277 351 217 148 98 48 28 21 8 6 4 4 2 0 1
##
## $density
## [1] 1.141797e-02 1.446826e-02 8.944765e-03 6.100577e-03 4.039571e-03
## [6] 1.978566e-03 1.154163e-03 8.656224e-04 3.297609e-04 2.473207e-04
## [11] 1.648805e-04 1.648805e-04 8.244023e-05 0.000000e+00 4.122012e-05
##
## $mids
## [1] 10 30 50 70 90 110 130 150 170 190 210 230 250 270 290
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[8]][[10]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550
##
## $counts
## [1] 838 190 100 40 15 10 7 9 3 0 1
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## $density
## [1] 1.381698e-02 3.132729e-03 1.648805e-03 6.595218e-04 2.473207e-04
## [6] 1.648805e-04 1.154163e-04 1.483924e-04 4.946414e-05 0.000000e+00
## [11] 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[8]][[11]]
## $breaks
## [1] 0 100 200 300 400 500 600 700 800 900 1000 1100
##
## $counts
## [1] 1113 1 3 8 16 21 19 19 9 3 1
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## $density
## [1] 9.175598e-03 8.244023e-06 2.473207e-05 6.595218e-05 1.319044e-04
## [6] 1.731245e-04 1.566364e-04 1.566364e-04 7.419621e-05 2.473207e-05
## [11] 8.244023e-06
##
## $mids
## [1] 50 150 250 350 450 550 650 750 850 950 1050
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
##
## [[9]]
## [[9]][[1]]
## $breaks
## [1] 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85
##
## $counts
## [1] 5 13 15 19 36 57 54 81 107 144 154 210 184 99 29 4 2
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## $density
## [1] 0.0008244023 0.0021434460 0.0024732069 0.0031327288 0.0059356966
## [6] 0.0093981863 0.0089035449 0.0133553174 0.0176422094 0.0237427865
## [11] 0.0253915911 0.0346248969 0.0303380049 0.0163231657 0.0047815334
## [16] 0.0006595218 0.0003297609
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## $mids
## [1] 2.5 7.5 12.5 17.5 22.5 27.5 32.5 37.5 42.5 47.5 52.5 57.5 62.5 67.5 72.5
## [16] 77.5 82.5
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## $mids
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## $xname
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## $equidist
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## attr(,"class")
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## $mids
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## $xname
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## $equidist
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## $mids
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## $xname
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## $equidist
## [1] TRUE
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## attr(,"class")
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## $mids
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## $xname
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## $equidist
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## $xname
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## $equidist
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## [[9]][[7]]
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## $mids
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## $xname
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## $equidist
## [1] TRUE
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## [1] "histogram"
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## $mids
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## $xname
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## $equidist
## [1] TRUE
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## [1] "histogram"
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[9]][[10]]
## $breaks
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## $mids
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## $xname
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## $mids
## [1] 50 150 250 350 450 550 650 750 850 950
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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##
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## [[10]][[1]]
## $breaks
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## $density
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## $mids
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## $xname
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[10]][[2]]
## $breaks
## [1] 0 10 20 30 40 50 60 70 80 90 100
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## $counts
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## $density
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## $mids
## [1] 5 15 25 35 45 55 65 75 85 95
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## $mids
## [1] 10 30 50 70 90 110 130 150 170 190 210
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[10]][[4]]
## $breaks
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## $mids
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## $xname
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[10]][[5]]
## $breaks
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## $counts
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[10]][[6]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550 600 650
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## $counts
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[10]][[7]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550
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## $counts
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[10]][[8]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550 600 650
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525 575 625
##
## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
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## [[10]][[9]]
## $breaks
## [1] 0 20 40 60 80 100 120 140 160 180 200 220 240
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## $counts
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## $mids
## [1] 10 30 50 70 90 110 130 150 170 190 210 230
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[10]][[10]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550
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## $counts
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[10]][[11]]
## $breaks
## [1] 0 100 200 300 400 500 600 700 800 900 1000
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## $counts
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## $mids
## [1] 50 150 250 350 450 550 650 750 850 950
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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##
## [[11]]
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## $density
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
##
## [[11]][[2]]
## $breaks
## [1] 0 10 20 30 40 50 60 70 80 90 100
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## $counts
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## $density
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## $breaks
## [1] 0 20 40 60 80 100 120 140 160 180 200
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## $counts
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## $density
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## $mids
## [1] 10 30 50 70 90 110 130 150 170 190
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## $breaks
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[11]][[5]]
## $breaks
## [1] 0 50 100 150 200 250 300 350
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## $breaks
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## $counts
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[11]][[7]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450
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## $counts
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## $density
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## $mids
## [1] 25 75 125 175 225 275 325 375 425
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[11]][[8]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500
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## $counts
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## $mids
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## $breaks
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## $counts
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## $density
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## $mids
## [1] 10 30 50 70 90 110 130 150 170 190 210 230 250
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[11]][[10]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550 600
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## $counts
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## [6] 1.154163e-04 1.319044e-04 8.244023e-05 8.244023e-05 1.648805e-05
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## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525 575
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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## [[11]][[11]]
## $breaks
## [1] 0 100 200 300 400 500 600 700 800 900 1000
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## $counts
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## $density
## [1] 9.175598e-03 0.000000e+00 8.244023e-06 8.244023e-05 1.071723e-04
## [6] 2.061006e-04 1.813685e-04 1.401484e-04 9.068425e-05 8.244023e-06
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## $mids
## [1] 50 150 250 350 450 550 650 750 850 950
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## $xname
## [1] "X[[i]]"
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## $equidist
## [1] TRUE
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## attr(,"class")
## [1] "histogram"
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##
## [[12]]
## [[12]][[1]]
## $breaks
## [1] 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80
##
## $counts
## [1] 7 6 21 20 30 31 55 57 85 154 280 262 130 61 13 1
##
## $density
## [1] 0.0011541632 0.0009892828 0.0034624897 0.0032976092 0.0049464138
## [6] 0.0051112943 0.0090684254 0.0093981863 0.0140148392 0.0253915911
## [11] 0.0461665293 0.0431986810 0.0214344600 0.0100577082 0.0021434460
## [16] 0.0001648805
##
## $mids
## [1] 2.5 7.5 12.5 17.5 22.5 27.5 32.5 37.5 42.5 47.5 52.5 57.5 62.5 67.5 72.5
## [16] 77.5
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[12]][[2]]
## $breaks
## [1] 0 10 20 30 40 50 60 70 80 90 100 110
##
## $counts
## [1] 41 74 144 189 166 168 166 161 86 17 1
##
## $density
## [1] 3.380049e-03 6.100577e-03 1.187139e-02 1.558120e-02 1.368508e-02
## [6] 1.384996e-02 1.368508e-02 1.327288e-02 7.089860e-03 1.401484e-03
## [11] 8.244023e-05
##
## $mids
## [1] 5 15 25 35 45 55 65 75 85 95 105
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[12]][[3]]
## $breaks
## [1] 0 20 40 60 80 100 120 140 160 180 200
##
## $counts
## [1] 267 325 242 144 117 63 26 14 13 2
##
## $density
## [1] 1.100577e-02 1.339654e-02 9.975268e-03 5.935697e-03 4.822754e-03
## [6] 2.596867e-03 1.071723e-03 5.770816e-04 5.358615e-04 8.244023e-05
##
## $mids
## [1] 10 30 50 70 90 110 130 150 170 190
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[12]][[4]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400
##
## $counts
## [1] 782 291 81 35 10 7 6 1
##
## $density
## [1] 1.289365e-02 4.798021e-03 1.335532e-03 5.770816e-04 1.648805e-04
## [6] 1.154163e-04 9.892828e-05 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[12]][[5]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450
##
## $counts
## [1] 804 255 92 34 12 8 3 4 1
##
## $density
## [1] 1.325639e-02 4.204452e-03 1.516900e-03 5.605936e-04 1.978566e-04
## [6] 1.319044e-04 4.946414e-05 6.595218e-05 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375 425
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[12]][[6]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500
##
## $counts
## [1] 806 242 100 36 13 9 2 3 1 1
##
## $density
## [1] 1.328937e-02 3.990107e-03 1.648805e-03 5.935697e-04 2.143446e-04
## [6] 1.483924e-04 3.297609e-05 4.946414e-05 1.648805e-05 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375 425 475
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[12]][[7]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500
##
## $counts
## [1] 808 247 87 36 13 13 5 2 1 1
##
## $density
## [1] 1.332234e-02 4.072547e-03 1.434460e-03 5.935697e-04 2.143446e-04
## [6] 2.143446e-04 8.244023e-05 3.297609e-05 1.648805e-05 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375 425 475
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[12]][[8]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550
##
## $counts
## [1] 810 231 98 44 17 7 3 1 1 0 1
##
## $density
## [1] 1.335532e-02 3.808739e-03 1.615829e-03 7.254740e-04 2.802968e-04
## [6] 1.154163e-04 4.946414e-05 1.648805e-05 1.648805e-05 0.000000e+00
## [11] 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[12]][[9]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450
##
## $counts
## [1] 734 364 84 23 6 1 0 0 1
##
## $density
## [1] 1.210223e-02 6.001649e-03 1.384996e-03 3.792251e-04 9.892828e-05
## [6] 1.648805e-05 0.000000e+00 0.000000e+00 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375 425
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[12]][[10]]
## $breaks
## [1] 0 50 100 150 200 250 300 350 400 450 500 550 600 650
##
## $counts
## [1] 826 218 80 45 18 7 6 5 4 1 2 0 1
##
## $density
## [1] 1.361913e-02 3.594394e-03 1.319044e-03 7.419621e-04 2.967848e-04
## [6] 1.154163e-04 9.892828e-05 8.244023e-05 6.595218e-05 1.648805e-05
## [11] 3.297609e-05 0.000000e+00 1.648805e-05
##
## $mids
## [1] 25 75 125 175 225 275 325 375 425 475 525 575 625
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
##
## [[12]][[11]]
## $breaks
## [1] 0 100 200 300 400 500 600 700 800 900
##
## $counts
## [1] 1113 0 0 5 15 27 28 19 6
##
## $density
## [1] 9.175598e-03 0.000000e+00 0.000000e+00 4.122012e-05 1.236603e-04
## [6] 2.225886e-04 2.308326e-04 1.566364e-04 4.946414e-05
##
## $mids
## [1] 50 150 250 350 450 550 650 750 850
##
## $xname
## [1] "X[[i]]"
##
## $equidist
## [1] TRUE
##
## attr(,"class")
## [1] "histogram"
Skewness <- data.frame("Skewness"=as.vector(pbsapply(scores, function(x) sapply(x, skewness))),
"Dropout"=rep(dropout_percent, each=length(dim_val)),
"Dimension"=dim_val)
ggplot(Skewness, aes(x=Dimension, y=Skewness)) +
geom_line(aes(group=Dropout)) +
geom_point(aes(color=Dropout))
Antihub <- data.frame("Antihub"=as.vector(pbsapply(scores, function(x) sapply(x, antihub))),
"Dropout"=rep(dropout_percent, each=length(dim_val)),
"Dimension"=dim_val)
ggplot(Antihub, aes(x=Dimension, y=Antihub)) +
geom_line(aes(group=Dropout)) +
geom_point(aes(color=Dropout))
KThd <- data.frame("KThd"=as.vector(pbsapply(scores, function(x) sapply(x, function(y) k_thd(y,k)))),
"Dropout"=rep(dropout_percent, each=length(dim_val)),
"Dimension"=dim_val)
ggplot(KThd, aes(x=Dimension, y=KThd)) +
geom_line(aes(group=Dropout)) +
geom_point(aes(color=Dropout))
MeanSdThd <- data.frame("MeanSdThd"=as.vector(pbsapply(scores, function(x) sapply(x, meansd_thd))),
"Dropout"=rep(dropout_percent, each=length(dim_val)),
"Dimension"=dim_val)
ggplot(MeanSdThd, aes(x=Dimension, y=MeanSdThd)) +
geom_line(aes(group=Dropout)) +
geom_point(aes(color=Dropout))
Asymmetry <- data.frame("Asymmetry"=as.vector(pbsapply(scores, function(x) sapply(x, asymmetry_evaluation))),
"Dropout"=rep(dropout_percent, each=length(dim_val)),
"Dimension"=dim_val)
ggplot(Asymmetry, aes(x=Dimension, y=Asymmetry)) +
geom_line(aes(group=Dropout)) +
geom_point(aes(color=Dropout))
rc <- pbsapply(simul_pca, function(x) sapply(dim_val, function(y) relative_contrast(x[1:y,])))
link_df <- data.frame("Relative_contrast"=as.vector(rc),
"Asymmetry"=Asymmetry$Asymmetry,
"Skewness"=Skewness$Skewness,
"Dimension"=dim_val,
"Dropout"=rep(dropout_percent, each=length(dim_val)))
lm <- lm(Skewness ~ log(Relative_contrast), data=link_df)
summary(lm)
##
## Call:
## lm(formula = Skewness ~ log(Relative_contrast), data = link_df)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.40781 -0.64339 -0.00547 0.52833 2.69159
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 2.06937 0.07535 27.46 <2e-16 ***
## log(Relative_contrast) -0.43186 0.02712 -15.92 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.8657 on 130 degrees of freedom
## Multiple R-squared: 0.661, Adjusted R-squared: 0.6584
## F-statistic: 253.5 on 1 and 130 DF, p-value: < 2.2e-16
ggplot(link_df, aes(x=log(Relative_contrast), y=Skewness, color=Dropout)) +
geom_point() +
geom_abline(slope = lm$coefficients[2], intercept = lm$coefficients[1], color="red")
# Do pearson and spearman also
lm <- lm(Asymmetry ~ log(Relative_contrast), data=link_df)
summary(lm)
##
## Call:
## lm(formula = Asymmetry ~ log(Relative_contrast), data = link_df)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.143e-15 -3.833e-16 -1.784e-16 3.770e-17 2.434e-14
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.000e+00 1.902e-16 5.256e+15 <2e-16 ***
## log(Relative_contrast) 1.562e-16 6.848e-17 2.281e+00 0.0242 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 2.186e-15 on 130 degrees of freedom
## Multiple R-squared: 0.4998, Adjusted R-squared: 0.496
## F-statistic: 129.9 on 1 and 130 DF, p-value: < 2.2e-16
ggplot(link_df, aes(x=log(Relative_contrast), y=Asymmetry, color=Dropout)) +
geom_point() +
geom_abline(slope = lm$coefficients[2], intercept = lm$coefficients[1], color="red")
